Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
JUNB

Cell type

Cell type Class
Breast
Cell type
MDA-MB-231
Primary Tissue
Breast
Site of Extraction
Effusion, Pleural
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
Breast cancer cell line
cell type
MDA-MB-231 cells
transformation status
--
chip antibody
JUNB (Cell Signaling Technology, 3753s)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were dual cross-linking with a mixture of 2 mM each of ethylene glycol bis (succinimidyl succinate) (EGS) and disuccinimidyl glutarate (DSG) and 1% formaldehyde. Chromatin was digested with 60 units MNase (New England Biolabs, M0247S) at 37 0C for 10 minutes and then sonicated using Branson Microtip Sonifier 450 (4X15 second at output 4.5 and duty cycle 60%) to the sizes mostly between 150-500 bp. 50 μg chromatin, antibodies for transcription factors (listed in Table S6), and 15 μl Dynabead protein G (Thermo Fisher Scientific, 10004D) was used for the chromatin immunoprecipitation (ChIP)

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
22990989
Reads aligned (%)
59.4
Duplicates removed (%)
8.3
Number of peaks
40241 (qval < 1E-05)

hg19

Number of total reads
22990989
Reads aligned (%)
59.1
Duplicates removed (%)
9.1
Number of peaks
40189 (qval < 1E-05)

Base call quality data from DBCLS SRA